Atomistry » Magnesium » PDB 3igi-3is5 » 3iki
Atomistry »
  Magnesium »
    PDB 3igi-3is5 »
      3iki »

Magnesium in PDB 3iki: 5-Sme-Du Containing Dna Octamer

Protein crystallography data

The structure of 5-Sme-Du Containing Dna Octamer, PDB code: 3iki was solved by J.Sheng, A.E.A.Hassan, W.Zhang, J.Gan, Z.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.32 / 1.38
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 42.882, 42.882, 23.687, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 19.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the 5-Sme-Du Containing Dna Octamer (pdb code 3iki). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the 5-Sme-Du Containing Dna Octamer, PDB code: 3iki:

Magnesium binding site 1 out of 1 in 3iki

Go back to Magnesium Binding Sites List in 3iki
Magnesium binding site 1 out of 1 in the 5-Sme-Du Containing Dna Octamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of 5-Sme-Du Containing Dna Octamer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg11

b:31.3
occ:1.00
OP2 A:DG3 2.1 16.5 1.0
O A:HOH36 2.6 22.0 1.0
O A:HOH45 2.7 23.7 1.0
P A:DG3 3.4 15.7 1.0
C8 A:DG3 3.4 10.0 1.0
C3' A:UMS2 3.5 10.5 1.0
C5' A:DG3 3.5 13.7 1.0
O A:HOH32 3.7 20.0 1.0
N7 A:DG3 3.9 9.9 1.0
O3' A:UMS2 3.9 12.8 1.0
O5' A:DG3 3.9 15.2 1.0
O5' A:UMS2 4.1 8.9 1.0
C6 A:UMS2 4.1 9.1 1.0
C2' A:UMS2 4.2 10.0 1.0
O4' A:DG3 4.4 12.4 1.0
C5 A:UMS2 4.5 9.6 1.0
N1 A:UMS2 4.6 9.2 1.0
C4' A:DG3 4.6 13.2 1.0
O A:HOH26 4.6 21.2 1.0
OP2 A:UMS2 4.6 10.5 1.0
N9 A:DG3 4.6 10.2 1.0
C4' A:UMS2 4.6 9.1 1.0
OP1 A:DG3 4.7 17.1 1.0
C5' A:UMS2 4.8 8.8 1.0
C1' A:UMS2 4.9 8.9 1.0
P A:UMS2 4.9 9.1 1.0

Reference:

J.Sheng, W.Zhang, A.E.Hassan, J.Gan, A.S.Soares, S.Geng, Y.Ren, Z.Huang. Hydrogen Bond Formation Between the Naturally Modified Nucleobase and Phosphate Backbone. Nucleic Acids Res. V. 40 8111 2012.
ISSN: ISSN 0305-1048
PubMed: 22641848
DOI: 10.1093/NAR/GKS426
Page generated: Wed Aug 14 16:11:34 2024

Last articles

Cl in 2QUJ
Cl in 2QVZ
Cl in 2QVY
Cl in 2QVB
Cl in 2QVX
Cl in 2QU7
Cl in 2QU6
Cl in 2QTS
Cl in 2QT6
Cl in 2QU5
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy